missing ctest and methodological question

Christof Meigen <cmeigen at gmx.de> writes:

I couldn't figure out how to use the functions from the
ctest library. I'm using the r-base package that comes with
debian potato. library("ctest") told me that no such package
existed. I checked the CRAN, but no such package was
availiable, instead I was told that it would be part of the
standard installation. But functions from ctest like
shapiro-wilk don't work.  The only thing I found was a
ASCII-file "ctest" which I could load but was only a wrapper
for some C-Library which seems to be not installed.

Because of the very long delays between the freezing of a Debian
distribution and its eventual release, versions of r-base on Debian
releases are woefully out of date.  I think the version of r-base in
the Debian potato release is 0.90.x while the current released version
of R is 1.2.2 (and 1.2.3 is imminent).  The ctest package is included
with recent versions of R.  In particular it is included with the
Debian packages for r-base_1.2.2 that you can download from

              http://cran.r-project.org/bin/linux/debian

(You can substitute a CRAN mirror site for cran.r-project.org)

The ReadMe file in that directory gives instructions on how to
configure apt, Debian's advanced package tool, to search for packages
in that location automatically.
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Christof,

For the first part of your question:

If you got your r-base from a CD distribution of potato, the version of
r-base could be very old (I have one here that has R version .90 on it).  
Even the debian mirror I use has R at version .90.  If that's true your
version won't automatically load ctest (you would have to "library(ctest)"
to use the features).  In version 1.2.2 ctest is loaded automatically at
startup.  I get my debian packages of r-base and r-doc from the CRAN site.  
Those are current.  You can download a copy of r-base*.deb from CRAN and
install it by hand with dpkg, or you can also point apt-get at:

http://cran.r-project.org/linux/debian/dists/stable/main

and apt will install it for you. 


Hope this helps, 

Scot

--
  Scot W. McNary  email:smcnary at charm.net

Hi,

I couldn't figure out how to use the functions from the
ctest library. I'm using the r-base package that comes with
debian potato. library("ctest") told me that no such package
existed. I checked the CRAN, but no such package was
availiable, instead I was told that it would be part of the
standard installation. But functions from ctest like
shapiro-wilk don't work.  The only thing I found was a
ASCII-file "ctest" which I could load but was only a wrapper
for some C-Library which seems to be not installed.

Besides that technical problem I would also appreciate your
scientific advice. For a publication a have to check about
80 samples with about 3000-5000 values each whether they
a normally distributed (N(0,1) to be exact). The problem is,
that they are derived from discrete measurements (the
weight of children, for example, where nearly all values
have full or half kilograms), so Kolmogorov-Smirnov doesn't
seem to be the right choice. Shapiro-Wilk, however,
is limites to 5000 values, for good reasons, I think.

Personally, for a single sample I would make some plots
for everyone to see that it fits quite good, but in this
case it would be nice if I could finally have a table
saying

sample  test1   test2  ...
1       accept  accept
2       accept  reject
...

any advices about which tests I could perform?

Thanks in advance,
        Christof
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Hi,

I couldn't figure out how to use the functions from the
ctest library. I'm using the r-base package that comes with
debian potato. library("ctest") told me that no such package
existed. I checked the CRAN, but no such package was
availiable, instead I was told that it would be part of the
standard installation. But functions from ctest like
shapiro-wilk don't work.  The only thing I found was a
ASCII-file "ctest" which I could load but was only a wrapper
for some C-Library which seems to be not installed.

It's been a long time so I'm not sure, but it may be that the version of R
in 'potato' precedes the addition of ctest to the base package.  In any
case you want to upgrade, and I haven't heard of library("ctest") not
working on any recent systems (in fact we have people complaining that
they can't get rid of it...)

Besides that technical problem I would also appreciate your
scientific advice. For a publication a have to check about
80 samples with about 3000-5000 values each whether they
a normally distributed (N(0,1) to be exact). The problem is,
that they are derived from discrete measurements (the
weight of children, for example, where nearly all values
have full or half kilograms), so Kolmogorov-Smirnov doesn't
seem to be the right choice. Shapiro-Wilk, however,
is limites to 5000 values, for good reasons, I think.

Well, if they are discrete then they *aren't* normally distributed. Even
the Shapiro-Wilk test will reject for discretised Normal data, though
slightly less powerfully than the Kolmogorov-Smirnov.

You could try the skewness and kurtosis based tests of normality, or you
could write a function that computes the CDF of a suitably discretised
Normal distribution and compare your data to that using ks.test(), which
allows you to specify any CDF.  This is slightly cheating as you will
presumably be using estimated parameters in computing this CDF, but with
3000 cases it should all come out in the wash.

This is all based on the assumption that you do in fact want a normality
test, an assumption I am usually suspicious of...


	-thomas

Thomas Lumley			Asst. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle

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Hi,

thanks to all who replied, installing the new R-version
from CRAN solved the problem with ctest.

Thanks especially to Thomas Lumley -- I think I'll try that
test with a discretised Normal distribution.

        Christof
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